Stargate:Atlantis Season:6 Epi 1 Distant Threats
by USS Thor
Summary: While on Earth the Atlantis team makes a discovery
1. Chapter 1

Stargate Atlantis Season 6 Episode 1 "Distant Threats Part 1"

As John Sheppard sat in his quarters aboard Atlantis he wondered how even though he was back on Earth again that he didn't seem to enjoy all of the oversight the IOA and the bureaucrats had over everything. No soldier likes to risk his life on every mission they go on but he had become accustomed to the thrill of life in the Pegasus galaxy. Without the Goa'uld or the Ori threatening the galaxy life around the SGC had become a bit stagnant. Every mission was either escorting scientists to examine ruins of an ancient city or First Contact. While first contact can be exciting most of the people they met were still primitive. Meanwhile Rodney was in charge of unlocking all of Atlantis's wonders so he was busy but even he missed the action that even though he feared he had grown used to. Ronan was finding it especially difficult to fit in because while he considered his team family, he knew there was still Wraith that were feeding in Pegasus and couldn't stand the thought of being helpless to do anything. Teyla adapted well enough that she could go out shopping among the people without standing out much like Teal'c had done before. Kanaan was having issues however; he missed his fellow Athosians that were still back in Pegasus. Teyla understood but the longer they stayed on Earth the farther she felt him grow away from her. Meanwhile Ronan and Amelia were sparring in the gym and were going at it pretty intensely. Eventually it led to passionate kissing which led them back to Ronan's quarters for a night of passion. Teyla and John were eating lunch together in the mess hall. "John, I feel Kanaan pulling away from my but everything I have tried has failed, what I do?" she asked.

"Well have you tried talking to him about why he's being distant" he asked. She then gave him a stare that was enough to tell him that it was a pointless question.

"Ok ok sorry I'm just not real good at the relationship problems kind of thing Teyla. Maybe you should try Dr. Keller" he suggested.

"Yes maybe that would be wise, I hear her and McKay are having problems of their own as well" replied Teyla

" Yeah Rodney is being well Rodney which would be a problem for anyone, I respect her though since she is living what I would consider my worst nightmare" said John with a smirk.

"So John how about you?" asked Teyla and John looked at her with a confused look on his face and then Teyla said "You know seeing anybody? Every since we've been back on Earth it seems everyone was reunited with their loved ones".

"Oh no not me, I stop in to see my family from time to time but no theirs not anyone I'm involved with" he said and looked at Teyla directly into the eyes and said "You know me I kind of have a thing for women from other planets" The two shared a very intense and flirty state.

"Well Teyla I have some work to do and we have that mission to P4A-571 tomorrow so I better get ready." He got up and started to walk away when Teyla thanked him for the Talk and the help he meant to give her. The Mission to P4A-571 was just going to be a standard Recon and search for the possibility of Naquadah. Without the threat of attack the leaders of Earth thought that setting up off world bases and mines would help the fleet grow and protect Earth from the growing size of the Lucian Alliance. As John walked down the hall and to his quarters he couldn't help but think to himself that maybe he and Teyla could have had something in the past. He had thought about it and obviously everyone saw that they cared for each other especially Ronan. He brushed the thought off since he didn't want to play homewrecker especially since to Teyla family was much more important then people on Earth believed it to be. Over in McKay's lab he was busy working trying to figure out a way to get Atlantis back to Pegasus without depleting the city's ZPM's. Jennifer was bringing him lunch to surprise him and try to get him to go to dinner with her father who had flown out to meet with her. "Rodney guess what I have" she said as she held a picnic basket in her hand

" Thank god I'm starving" he said as he reached out for the basket.

"Not uh, not so fast, before I give this to you I have a question to ask you first" she said.

"Ok ask away" he said as he kind of danced like a kid who has to use the bathroom as he waited impatiently.

"My dad is coming to San Francisco to have dinner with me, I'd like for you to come and meet him" she said nervously.

"Uh uh uh your dad?" he stuttered looking scared.

"Rodney we've been dating for about a year now, Don't you think it's time to take things to the next level?" she asked him. 

"Yeah i'd like that" he said but in his head he was terrified. What if her dad didn't like him? What if she found somebody better? He knew that he was far from the John Sheppard's of the World. She got the awnser she wanted and handed him the picnic basket and he immediately started to unpack it and set it up on his table. He started to tell her about how his work was coming and she pretended to be interested but she just wanted to enjoy time with him away from work. She fell for the nice guy Rodney could be but she also saw the stubborn side that could push her away when he'd get caught up in his work and miss dates they had planned. They ate lunch together but she could barely get a word in as Rodney was talking about his idea to us to get Atlantis back to Pegasus. She left the lab and headed back to infirmary.


	2. Chapter 2

As Jennifer walked down the corridor headed back to the infirmary Teyla rounded the corner and caught up to her. "Dr. Keller do you have a minute to talk?" Teyla asked.

"Yes Teyla, what's wrong? Are you feeling ok?" asked Dr. Keller

"Yes I am Fine but I was wondering if you could offer me some advice on relationships" responded Teyla.

"I'm not sure how much help I'll be Teyla, My relationship knowledge is kind of limited, Remember I was usually much younger then my classmates and well Rodney isn't exactly your normal guy" she said as she kind of chuckled remembering Rodney's charm that she loved.

"Well since we have been back on Earth I find that Kanaan has been growing distant, I know he misses our people and worries for them. I do as well but with no way back I am unsure as to how worrying about it so strongly can do anything but make matters worse." Teyla said.

"Well I'm sure he feels homesick and I understand since when I first got to Atlantis I felt alone and isolated. I mean I was in a whole other galaxy with no family or friends around" answered Keller.

"But you made friends quickly with everyone on the base, Kanaan just sits in the room and cares for Torran but he only goes out to get food and to train in the gym. I try to ask him what's wrong but he just simply tells me he misses home and that is the end of the conversation" said Teyla

"Sounds to me that he just misses home and while he has you and Torran, he just doesn't have anyone else to talk to and maybe getting involved in some group activities would help" responded Keller.

"Thank You Jennifer" Teyla said and began to walk back to her quarters to meet up with Kanaan. Upon arriving back at her room she entered to see Kanaan holding Torran as he was asleep. She tried to talk to him and get him to open up but again he shut down and walked away from her. In her frustration she walked out and went down to the south-west pier. She stood on the balcony looking over at the Golden Gate Bridge and all the lights crossing it. This was far from the quiet worlds of Pegasus that she was used to. She lost track of time and when she got back Kannan and Torran were both asleep. She changed into her nightgown and crawled into bed with Kannan. As she drifted off to sleep she prayed for things to get better. The following morning she had slept through her alarm and John had to come get her up so they wouldn't be late for their mission. He waited as she quickly showered and geared up and when she talked out of her quarters he said "Rough night?"

"Yes I was restless because of Kanaan" she responded.

"Well look on the bright side we have an unknown planet to explore and who knows what could be there. Maybe something dangerous" he said with a smirk. They headed to the gate room where the Apollo beamed them to the first level of the SGC where they would take an elevator down to the briefing room. John missed the Atlantis uniforms but at least the SGC had switched to the respective branches camo. Everyone now downed the air force's camo uniforms except for Ronan which kept to his usual attire. They sat through the briefing that General Landry provided about the mission which was a basic recon to search for Naquadah. Earth was trying to find more Naquadah and trinium for construction of more 304 class ships. After the briefing the team headed down to the armory to gear up. Ronan had started to carry a P90 and 9mm pistol since he knew he trademark sidearm would eventually run out of energy so he used it only when needed. With the emerging threat of the Lucian Alliance all SG teams started to carry heavier weapons. While Teyla carried the standard P90 and 9mm pistol she also carried a UMP 45 for extra knockdown power. Even Rodney carried a MP5 in automatic pistol form along with the P90 and 9mm pistol. For John being home had a few advantages such as being able to have as many weapons as he wanted. He decided that a little extra weight might be worth it in case of emergency so he carried his P90 on his vest with two .45 1911 Pistols on his thigh and one in his vest. He also carried a M4 with a 203 grenade launcher with a 4x sight. For long distance threats he carried the new M1110 sniper rifle. Ronan would also carry a M60 machine gun if the MALP detected any kind of life that might be a threat. Sheppard looked at Ronan and said "Ready Chewie?" and laughed as he walked by and tapped him on the shoulder.

"You know Sheppard I'd prefer to be back in Pegasus killing Wraith and not searching for minerals and other useless things" responded Ronan.

"I know how ya feel buddy but until we can find a way back without draining the ZPM's were stuck" responded Sheppard.

"This may sound strange but I miss it too" chimed in Rodney. They walked into the Gateroom as the gate was dialing for P4A-571. The wormhole engaged and the team turned to look at General Landry in the control room.

"AR-1 you have a go, good luck" said the General. With that the team headed through the gate. After arriving on P4A-571 the team radioed back to Stargate Command that the planet seemed quiet and that they'd radio back in 24 hours. Back on Earth Richard Woolsey was finding his job of getting Atlantis space worthy again a boring task. After all the ancients had built this great city and now the SGC was adding rail gun emplacements as well as Asgard Plasma Beam Weapon platforms as a way to defend against attack in case the drones ran out. They were also adding Naquadah generators around the city so that the ZPM's would power just the shield and weapons. Radek was put in charge of the upgrades to make sure they would function properly. Not shortly there after AR-1 left for their mission, the Apollo left orbit to meet up with the General Hammond. That left only the Daedalus in orbit while the Odyssey was away on a top secret mission that only General Landry and General O'Neil knew about. 


	3. Chapter 3

As Sheppard and the team came through the gate they were surrounded by a thick dense jungle that has almost overtaken the stargate and the platform that the gate rests on. It is around 7pm on the plant and the team notices that the sun is starting to set.

"We better set up camp for the night and McKay get everything set up for the scans to test for naquadah" Ordered John.

"Ok it'll take me 20 minutes tops" responded McKay

"Teyla, Ronan work on getting a security perimeter set up, give me a standard perimeter" ordered Sheppard. 

With that Teyla and Ronan moved off into the forest to set up claymore mines and motion detectors. As McKay was working on calibrating the scanners calibrated it started to pour down raining.

"Just great, why can't it ever be a warm sunny climate" he thought to himself. The rain was so heavy that before they could get their rain gear on their clothes were soaked to the core.

"Looks like were in for a long night" said Teyla with a grin on her face.

"Yeah lets just get some sleep, I and Ronan will take first watch, and we'll wake you two in 4 hours" John Said.

"Ok John, Night Ronan" responded Teyla.

Rodney and Teyla crawled into their tents where it was dry and Rodney laid there thinking of being back in Atlantis with Jennifer in bed warm and dry, Meanwhile Teyla thought about what she was going to do with Kanaan and herself. As Ronan and Sheppard watched they quietly discussed everything from how Ronan was adapting to life at the SGC and life on Earth to John's love life or lack thereof. Hours went by and all they heard was the sound of the rain and after the 4 hours they woke Teyla and McKay.

"It's been 4 hours already!" exclaimed McKay as he whined that he didn't get the full 8 hours he had grown accustomed.

"Suck it up McKay' shouted John as Ronan and Teyla gave each other a smile with a grin. Teyla and McKay spent the 4 hours they had on watch in silence since Rodney was too busy whining and complaining to himself. They woke Sheppard and Ronan as sunrise was occurring. They team packed up their camp and headed off as McKay used his handheld scanner to search for signs of the precious minerals they seek. After walking for 3 hours they finally came to a clearing in the jungle. They looked at each other in disbelief as the clearing was a perfect circle that was just big enough for an Alkesh to land. They immediately started searching the surrounding area for signs that they were not alone. After their search turned up nothing they headed across the clearing and back into the jungle. About 200 meters into the jungle they noticed that they were coming to a cliff edge, they approached and looked at each other in shock as they saw a old Goa'uld mining facility in full swing.

"Down, Down!" ordered Sheppard. The team dropped and John pulled out his binoculars and began to check out what was going on. It appeared to be a Lucian Alliance camp since the remaining Goa'uld were on Earth under the watchful eye of the IOA. As Sheppard scanned he found a figure who was giving commands, he was dressed in a leather outfit and had a ribbon device on one hand. His eyes glowed and John his team to fall back into the forest and head for the gate. As they came to the edge of the forest and came upon the clearing they noticed a Troop Transport decloak. Soldiers came out of it and the surrounding woods to surround the team.

" Drop your weapons Tau'ri scum" ordered a Tall dark skinned soldier.

"Crap" remarked John as he lowered his weapons and puts his hand in the air. He looked at the rest of his team as he was doing this and ordered them to do the same. The soldiers seized their weapons and escorted them into the Troop Transport. The Transport lifted off and headed towards the mining camp.

"Just another standard Mineral survey huh, Go Figure" whined McKay. The team just looked at him and he responded " What?" The team just shook their heads. 


	4. Chapter 4

The troop transport flew across the sky towards the Mining Site and the team awaited their fate. The ship landed in the middle of a landing site and as the team was pushed out of the transport they were shocked at what they saw. Apparently the part of the mining camp they saw from the cliff ledge was only the tip of the iceberg, as they looked around they saw over 30 pyramids and tons of cargo ships.

"My god I think we found the main mining outpost for the Lucian Alliance" Rodney said

"Quiet scum" a guard said as he smacked Rodney with his weapon.

"Ouch" whined Rodney. The team was forcibly led inside the largest pyramid where they came before a beautiful blonde woman.

"What is your purpose for being on this planet" she demanded.

"Oh you know just an adventure to an unknown planet trying to find the perfect vacation spot" replied John with a tone of sarcasm and a smirk on his face.

"Quiet, I already know your reason for coming here and who you are. You see John Sheppard we have our spies within your stargate program" replied the blonde woman. 

"Well if you knew then why did you ask?" asked the Col.

"I brought you here to show you that your world will soon cease to exist" replied the Blonde as her eyes flashed with a glow.

"You're a Goa'uld" replied Rodney

"I am Athena and you will find that I am not going to be overconfident when it comes to dealing with your world. You will come with me" she said as she looked at John.

She led the Col. Outside the pyramid and ordered one of the guards to give the order and John stared in disbelief as what seemed to be a hundred ha'tak shipyards decloaked. 

"You see I know the system lords underestimated your planet and I will not make that mistake" replied Athena. Then they got into a cargo ship and took off and headed out into space and when the ship came to a stop he watched as a combination of Ha'taks decloaked along with other ships that he never recognized.

"I captured you and your team so that you may witness the fleet that will destroy your planet and when we are done with earth it will be the Lucian Alliance and Aschen that will rule the galaxy with the leadership of the Goa'uld" snapped the woman. 

The ship then broke orbit and headed back towards the planet and Sheppard took a peak at the sensors and saw that the mining camp was just one of many on the planet. The ship landed and they led Sheppard back to the rest of his team.

"You see now that the Tauri's time as the dominant power in the galaxy will come to an end. I know that your precious Atlantis is on Earth and that is why I have assembled a combined fleet that will first destroy your cities and then we will capture Atlantis and learn all the secrets of the ancients" Commented the blonde woman. The team all looked at each other with a look of worry on their faces.

"You will head back to earth and inform your leaders of the impending attack" ordered Athena.

"Doesn't make a lot of sense to warn us of the attack now does it" replied John

" You see there is nothing you can do to stop us so now that you know I don't have to worry about having any more spies trying to get information, I grow tired of killing them" she replied.

The team was then stunned with Zats and were put in a cargo ship and then left back at their original campsite along with all of their weapons. They awoke groggy and to find that the SG team led by Alice Cantwell.

"Colonel is you alright" asked the young Captain

"Captain Cantwell what are you doing here" asked John

"Sir we were sent to find you after you failed to check in, your 24 hours overdue" responded the Captain.

The team was helped up and they gathered their gear and headed off to the gate which was still a few hours away.

"So does the planet have anything of value" asked Alice

"Captain this planet is now the single largest threat to earth, the Lucian Alliance have a major shipyard and mining operation" responded Col. Sheppard

"Sir we are only 150 light years from Earth, how could they do this right under our noses" she asked

"They seem to have learned how to cloak much of their technology." He responded

after hours of walking the teams arrived back at the gate. Rodney dialed the DHD and Capt. Cantwell put her Iris code in and the team stepped through the gate and headed back to Earth.


	5. Chapter 5

As the teams arrived back on Earth they were greeted by General Landry who asked them why they were late to check in and ordered them to the showers and be ready to debrief in 1 hour. The team headed off to the locker rooms where Rodney, Ronan and John ran into Col Reynolds of SG-3.

"How was P4A-571?" asked Col. Reynolds

"Oh you know just your typical run of the mill standard recon" responded Col. Sheppard in a sarcastic tone.

"Yeah I know what you mean" said Reynolds with a smirk.

They team all showered and changed into their standard black uniforms that were now being used for when the team was on base. They headed up to the conference table for debriefing. General Landry entered and sat at the head of the table.

"So what happened that caused you to fail with your scheduled check in?" asked Landry

"Sir we found that the Lucian Alliance has a base on the planet and it is building more ships and has a major mining outpost there" answered John.

"Shipyard? How big?" asked the general.

"Big!" exclaimed McKay

"General the shipyard is the biggest we've seen to date and they have the whole planet set up to mine the resources" said John.

"If I may General they said they have spies within the SGC" responded McKay

"Their warriors seem quite capable" chimed in Teyla

"Speak for yourself" said Ronan.

"Sir the Goa'uld Athena is leading them, she showed me the entire network, she said they are planning an attack on Earth and that they want to capture Atlantis" informed Sheppard

"Atlantis? What would they want with Atlantis?" asked the General

"The same thing we wanted" responded McKay

"We currently don't have enough power to get Atlantis back to Pegasus" responded Landry

"I've been working on that" answered McKay

"And what have you come up with so far" asked Landry as the rest of the team looked at him.

"If we could interface enough Naquaduh generators so that the ZPM's would power just the engines then we would have enough power to reach Pegasus but it would leave very little energy left in the ZPM's" answered McKay

"How many generators would you need" asked the General

"Roughly 100 give or take" responded McKay

"Get it done then McKay, The Odyssey is currently away on a mission but when she returns I am sending the rest of your team to Pegasus to set up a Alpha site so we can see what is going on in Pegasus. "Said General Landry

The team looked at each other shocked that the plan to return Atlantis to Pegasus was being so easily considered. What they didn't know is that the IOA had already begun plans to return Atlantis to Pegasus since they figured the rewards of technology outweighed the risks of the wraith. General Landry ended the debriefing and immediately notified Home world Command and General O'Neil. The response was to put Earth and the off world bases on high alert for attacks. Everyone knew that if what Col. Sheppard saw as what they had plans that Earth could be in trouble.


End file.
